DNA-Corralled Nanodiscs for the Structural and Functional Characterization of Membrane Proteins and Viral Entry

Zhao, Zhao; Zhang, Meng; Hogle, James M.; Shih, William M.; Wagner, Gerhard; Nasr, Mahmoud L.

doi:10.1021/jacs.8b04638

Cited by 63 publications

(65 citation statements)

References 40 publications

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“…Conversely, molds can block unwanted interactions between independent assemblies. For example, here we show that lipid nanotubes can be templated inside but not outside the barrels, and we recently demonstrated scaffolding of large lipid nanodiscs inside of DNA-origami barrels 35 . This strongly suggests that the DNA barrel can act as a bumper to prevent unwanted aggregation of molecular assemblies hosted on the inside.…”

Section: Discussionmentioning

confidence: 61%

“…The cassette was floated in 2 L of reconstitution buffer for 48 h. After dialysis, the sample was recovered from the dialysis cassette and concentrated using an Amicon 30K column. Reconstituted nanostructures were separated from excess lipids by equilibrium centrifugation using iodixanol (Opti-Prep reagent, Sigma-Aldrich) gradient (35,28,18, and 8% from bottom to top). The gradient solutions were layered into ultracentrifuge tubes and centrifuged in Beckman SW41-Ti rotor at 287,730 g (41,000 rpm) for 5 h at 4°C.…”

Section: Methodsmentioning

confidence: 99%

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Complex multicomponent patterns rendered on a 3D DNA-barrel pegboard

et al. 2020

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DNA origami, in which a long scaffold strand is assembled with a many short staple strands into parallel arrays of double helices, has proven a powerful method for custom nanofabrication. However, currently the design and optimization of custom 3D DNA-origami shapes is a barrier to rapid application to new areas. Here we introduce a modular barrel architecture, and demonstrate hierarchical assembly of a 100 megadalton DNA-origami barrel of ~90 nm diameter and ~250 nm height, that provides a rhombic-lattice canvas of a thousand pixels each, with pitch of ~8 nm, on its inner and outer surfaces. Complex patterns rendered on these surfaces were resolved using up to twelve rounds of Exchange-PAINT super-resolution microscopy. We envision these structures as versatile nanoscale pegboards for applications requiring complex 3D arrangements of matter, which will serve to promote rapid uptake of this technology in diverse fields beyond specialist groups working in DNA nanotechnology.

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Section: Discussionmentioning

confidence: 61%

Section: Methodsmentioning

confidence: 99%

Complex multicomponent patterns rendered on a 3D DNA-barrel pegboard

et al. 2020

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“…These structures have been used for a range of applications. Control of bilayer shape has been used to wrap DNA nanostructures in a protective bilayer to prevent nuclease digestion and increase in vivo circulation time [24] and to assemble 2D DNA lipid 'nanodiscs' for the study of membrane protein interactions [129]. DNA-guided fusion has been used to bypass the endosomal pathway for delivery of proteins into live cells ( Figure 4A) [130] and to assemble biosensors for microRNA detection ( Figure 4B) [131].…”

Section: Bio-inspired Membrane Shapingmentioning

confidence: 99%

“…Multiple copies of these DNA-encircled bilayers can then be scaffolded into a larger DNA ring and fused by modulating detergent concentration to make a large, continuous bilayer of up to 70 nm. Large, DNA-supported 2D bilayers can also be created using this technique by scaffolding and fusing multiple protein lipid nanodiscs inside a DNA origami barrel [129].…”

Section: Directing Liposome Formationmentioning

confidence: 99%

The Fusion of Lipid and DNA Nanotechnology

Darley

Singh

Surace

et al. 2019

Genes

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Lipid membranes form the boundary of many biological compartments, including organelles and cells. Consisting of two leaflets of amphipathic molecules, the bilayer membrane forms an impermeable barrier to ions and small molecules. Controlled transport of molecules across lipid membranes is a fundamental biological process that is facilitated by a diverse range of membrane proteins, including ion-channels and pores. However, biological membranes and their associated proteins are challenging to experimentally characterize. These challenges have motivated recent advances in nanotechnology towards building and manipulating synthetic lipid systems. Liposomes—aqueous droplets enclosed by a bilayer membrane—can be synthesised in vitro and used as a synthetic model for the cell membrane. In DNA nanotechnology, DNA is used as programmable building material for self-assembling biocompatible nanostructures. DNA nanostructures can be functionalised with hydrophobic chemical modifications, which bind to or bridge lipid membranes. Here, we review approaches that combine techniques from lipid and DNA nanotechnology to engineer the topography, permeability, and surface interactions of membranes, and to direct the fusion and formation of liposomes. These approaches have been used to study the properties of membrane proteins, to build biosensors, and as a pathway towards assembling synthetic multicellular systems.

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“…By using DNA origami barrelsa ss caffolding corrals,Z hao et al reported a methodt om anufacture larger nanodisks through the assembly of small lipid-bilayern anodisks, which could open up to allow the addition of extra lipids. [44] In such aw ay,n anodisks with diameters as large as 70 nm have been achieved. With the coassembly of VDAC-1 proteins, densely packed membrane protein arrays may also be reconstituted within these large nanodisks.…”

Section: Self-assembly Of Lipids and Membrane Protein Scaffoldedthroumentioning

confidence: 99%

DNA Origami as Scaffolds for Self‐Assembly of Lipids and Proteins

Dong

Mao

2019

ChemBioChem

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Since first being reported in 2006, the DNA origami approach has attracted increasing attention due to programmable shapes, structural stability, biocompatibility, and fantastic addressability. Herein, we provide an account of recent developments of DNA origami as scaffolds for templating the selfassembly of distinct biocomponents, essentially proteins and lipids, into a diverse spectrum of integrated supramolecular architectures. First, the historical development of the DNA origami concept is briefly reviewed. Next, various applications of DNA origami constructs in controllable directed assembly of soluble proteins are discussed. The manipulation and self‐assembly of lipid membranes and membrane proteins by using DNA origami as scaffolds are also addressed. Furthermore, recent progress in applying DNA origami in cryoelectron microscopy analysis is discussed. These advances collectively emphasize that the DNA origami approach is a highly versatile, fast evolving tool that may be integrated with lipids and proteins in a way that meets future challenges in molecular biology and nanomedicine.

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DNA-Corralled Nanodiscs for the Structural and Functional Characterization of Membrane Proteins and Viral Entry

Cited by 63 publications

References 40 publications

Complex multicomponent patterns rendered on a 3D DNA-barrel pegboard

Complex multicomponent patterns rendered on a 3D DNA-barrel pegboard

The Fusion of Lipid and DNA Nanotechnology

DNA Origami as Scaffolds for Self‐Assembly of Lipids and Proteins

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